The filter does not set any margins, because the format does have no notion of "page", so this is either libodfgen default, libreoffice default or a bug in libodfgen in computing default margins. If it is not a bug in libodfgen, I'll just set all margins to 0.

I just found that after importing the pages have new style named PM2 instead of Default. Maybe this can help somehow.
Is it possible just set the Default style for FB2, as it done for plain text files (.txt), which are, by the way, also don't have any layout information?